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...olume images (i.e. that gives a sequence of 2D slices) such as magnetic resonance imaging (MRI), computed tomography (CT), single photon emission computed tomography (SPECT), or positron emission tomography (PET) can be adjusted to work on the FCC or BCC grids. For SPECT and CT, using the filtered back-projection method or direct Fourier method, the fact that the Fourier transform for the FCC and BCC grids (and for 2D planes that correspond to the 2D slices) exists is enough. Images on the FCC and BCC grids acquired using the algebraic reconstruction technique for SPECT or CT is found in Ref. [10]. They use spherically-symmetric volume elements (blobs) [11]. With the PET technique, the origin of gamma-rays (produced by annihilation of an emitted positron and an electron) are computed. The technique does not depend on the underlying grid except in the digitization step, which just as well can be performed on the FCC and BCC grids. Dealing with digital images means dealing with discrete grids. Indeed, digital images are discrete representation of the continuous world. Two kinds of approaches can be adopted to deal with discrete grids. The first one applies continuous methods to the discr...

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... to cope with these increasing computational efforts, most of these software packages have implemented parallel reconstruction algorithms to be used on various conventional parallel computing systems =-=[15, 8, 2, 22]-=-. Electron microscopy data are typically well suited for parallelization, since both images and processes can be treated independently, e.g. electron micrographs can be backprojected in a common three...

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...ed, bandpass filtered, centered, normalized and subjected to angular refinement. The raw data was analysed using reference-free alignment and classification methods implemented in EMAN (29) and XMIPP =-=(30)-=-. An initial 3D template for refinement was built using ‘startscym’ program implemented in EMAN (29) and the 6-fold symmetry of the molecule. BcMCM–ADP–ssDNA complex was obtained by incubating, in hex...

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...ate objective with an outermost zone width of drn = 40 nm, whereas a zone plate with drn = 25 nm was used for the acquisition of 4 datasets. The effective pixel sizes in the images were 15.6 nm or 8.6 nm (with the 40 nm zone plate objective, depending on the magnification), and 9.7 nm (with the 25 nm objective). The image stacks were pre-processed to normalize and correct the intensity distribution delivered to the sample by the capillary condenser using flat field images in a program developed for XMIPP3.0 software package (Marabini et al., 1996; Scheres et al., 2008; Schneider et al., 2010; Sorzano et al., 2004). Alignment of the tilted series was done with IMOD (Kremer et al., 1996), and the final reconstructions were performed using the iterative SIRT reconstruction option in TOMO3D (Agulleiro and Fernandez, 2011). To enhance the signal to noise levels we used TOMOBFLOW (Fernandez, 2009). The visualization and segmentation of the final volumes was carried out in Amira, IMOD and Chimera (Pettersen et al., 2004). The 3D-resolution estimation was done using the same approach as in Carrascosa et al. (2009). 2.6. Standard embedding For ultrastructural studies under electron microscopy, cells were cultu...

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...orted [3, 4]. But, so far the use of grids in 3D-EM has been limited. Over the past eight years, our group has been developing a program package for singleparticle 3D-EM image processing called Xmipp =-=[5]-=-. Whereas up to now its approach to highperformance computing has been based on MPI (message passing interface) implementations of the most time-consuming algorithms, current efforts have also address...

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...ts the L2-errors now in the presence of noise. Where the exact function to be projected is 17 defined by (7.1). In order to add Gaussian noise with the given signal-to-noise ratio (SNR), we use xmipp =-=[15]-=- package to compute the standard deviation for each given SNR value and then use the standard deviation to add Gaussian noise to each projection. For instance, for a SNR of 0.33, a total noise with a ...

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...ction The 3D reconstruction of icosahedral viruses was first introduced by Crowther et al. (1,2). There are numerous software packages such as Spider (30), IMAGIC (31), Frealign (32), PFT (33), XMIPP =-=(34)-=-, IMIRS (35), SAVR (11), and EMAN Fig. 3. Examples of particle selection. (A) automatically selected particles. (B) selected particles after manual screening. Cryo-EM of Viruses 353 Fig. 4. Contrast t...

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...pid construction of detailed models. The software packages mentioned above all assume the creation of a particular immutable model as their goal. As an example consider a script written for the XMIPP =-=[156, 157, 158]-=- text based phantom creation tool. An identical three dimensional model will be created each time the script is run because the script is unable to facilitate random effects in synthesised models. The...